src/gromacs/gmxana/princ.cpp

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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "princ.h"
  41
  42 #include <cmath>
  43
  44 #include "gromacs/linearalgebra/nrjac.h"
  45 #include "gromacs/math/vec.h"
  46 #include "gromacs/topology/topology.h"
  47 #include "gromacs/utility/smalloc.h"
  48
  49 #define NDIM 4
  50
  51 #ifdef DEBUG
  52 static void m_op(matrix mat, rvec x)
  53 {
  54     rvec xp;
  55     int  m;
  56
  57     for (m = 0; (m < DIM); m++)
  58     {
  59         xp[m] = mat[m][XX]*x[XX]+mat[m][YY]*x[YY]+mat[m][ZZ]*x[ZZ];
  60     }
  61     fprintf(stderr, "x    %8.3f  %8.3f  %8.3f\n", x[XX], x[YY], x[ZZ]);
  62     fprintf(stderr, "xp   %8.3f  %8.3f  %8.3f\n", xp[XX], xp[YY], xp[ZZ]);
  63     fprintf(stderr, "fac  %8.3f  %8.3f  %8.3f\n", xp[XX]/x[XX], xp[YY]/x[YY],
  64             xp[ZZ]/x[ZZ]);
  65 }
  66
  67 static void ptrans(char *s, real **inten, real d[], real e[])
  68 {
  69     int  m;
  70     real n, x, y, z;
  71     for (m = 1; (m < NDIM); m++)
  72     {
  73         x = inten[m][1];
  74         y = inten[m][2];
  75         z = inten[m][3];
  76         n = x*x+y*y+z*z;
  77         fprintf(stderr, "%8s %8.3f %8.3f %8.3f, norm:%8.3f, d:%8.3f, e:%8.3f\n",
  78                 s, x, y, z, std::sqrt(n), d[m], e[m]);
  79     }
  80     fprintf(stderr, "\n");
  81 }
  82
  83 void t_trans(matrix trans, real d[], real **ev)
  84 {
  85     rvec x;
  86     int  j;
  87     for (j = 0; (j < DIM); j++)
  88     {
  89         x[XX] = ev[1][j+1];
  90         x[YY] = ev[2][j+1];
  91         x[ZZ] = ev[3][j+1];
  92         m_op(trans, x);
  93         fprintf(stderr, "d[%d]=%g\n", j, d[j+1]);
  94     }
  95 }
  96 #endif
  97
  98 void principal_comp(int n, int index[], t_atom atom[], rvec x[],
  99                     matrix trans, rvec d)
 100 {
 101     int      i, j, ai, m, nrot;
 102     real     mm, rx, ry, rz;
 103     double **inten, dd[NDIM], tvec[NDIM], **ev;
 104 #ifdef DEBUG
 105     real     e[NDIM];
 106 #endif
 107     real     temp;
 108
 109     snew(inten, NDIM);
 110     snew(ev, NDIM);
 111     for (i = 0; (i < NDIM); i++)
 112     {
 113         snew(inten[i], NDIM);
 114         snew(ev[i], NDIM);
 115         dd[i] = 0.0;
 116 #ifdef DEBUG
 117         e[i] = 0.0;
 118 #endif
 119     }
 120
 121     for (i = 0; (i < NDIM); i++)
 122     {
 123         for (m = 0; (m < NDIM); m++)
 124         {
 125             inten[i][m] = 0;
 126         }
 127     }
 128     for (i = 0; (i < n); i++)
 129     {
 130         ai           = index[i];
 131         mm           = atom[ai].m;
 132         rx           = x[ai][XX];
 133         ry           = x[ai][YY];
 134         rz           = x[ai][ZZ];
 135         inten[0][0] += mm*(sqr(ry)+sqr(rz));
 136         inten[1][1] += mm*(sqr(rx)+sqr(rz));
 137         inten[2][2] += mm*(sqr(rx)+sqr(ry));
 138         inten[1][0] -= mm*(ry*rx);
 139         inten[2][0] -= mm*(rx*rz);
 140         inten[2][1] -= mm*(rz*ry);
 141     }
 142     inten[0][1] = inten[1][0];
 143     inten[0][2] = inten[2][0];
 144     inten[1][2] = inten[2][1];
 145 #ifdef DEBUG
 146     ptrans("initial", inten, dd, e);
 147 #endif
 148
 149     for (i = 0; (i < DIM); i++)
 150     {
 151         for (m = 0; (m < DIM); m++)
 152         {
 153             trans[i][m] = inten[i][m];
 154         }
 155     }
 156
 157     /* Call numerical recipe routines */
 158     jacobi(inten, 3, dd, ev, &nrot);
 159 #ifdef DEBUG
 160     ptrans("jacobi", ev, dd, e);
 161 #endif
 162
 163     /* Sort eigenvalues in ascending order */
 164 #define SWAPPER(i)          \
 165     if (std::abs(dd[i+1]) < std::abs(dd[i])) {    \
 166         temp = dd[i];         \
 167         for (j = 0; (j < NDIM); j++) { tvec[j] = ev[j][i]; } \
 168         dd[i] = dd[i+1];          \
 169         for (j = 0; (j < NDIM); j++) { ev[j][i] = ev[j][i+1]; }        \
 170         dd[i+1] = temp;           \
 171         for (j = 0; (j < NDIM); j++) { ev[j][i+1] = tvec[j]; }         \
 172     }
 173     SWAPPER(0)
 174     SWAPPER(1)
 175     SWAPPER(0)
 176 #ifdef DEBUG
 177     ptrans("swap", ev, dd, e);
 178     t_trans(trans, dd, ev);
 179 #endif
 180
 181     for (i = 0; (i < DIM); i++)
 182     {
 183         d[i] = dd[i];
 184         for (m = 0; (m < DIM); m++)
 185         {
 186             trans[i][m] = ev[m][i];
 187         }
 188     }
 189
 190     for (i = 0; (i < NDIM); i++)
 191     {
 192         sfree(inten[i]);
 193         sfree(ev[i]);
 194     }
 195     sfree(inten);
 196     sfree(ev);
 197 }
 198
 199 void rotate_atoms(int gnx, int *index, rvec x[], matrix trans)
 200 {
 201     real   xt, yt, zt;
 202     int    i, ii;
 203
 204     for (i = 0; (i < gnx); i++)
 205     {
 206         ii        = index ? index[i] : i;
 207         xt        = x[ii][XX];
 208         yt        = x[ii][YY];
 209         zt        = x[ii][ZZ];
 210         x[ii][XX] = trans[XX][XX]*xt+trans[XX][YY]*yt+trans[XX][ZZ]*zt;
 211         x[ii][YY] = trans[YY][XX]*xt+trans[YY][YY]*yt+trans[YY][ZZ]*zt;
 212         x[ii][ZZ] = trans[ZZ][XX]*xt+trans[ZZ][YY]*yt+trans[ZZ][ZZ]*zt;
 213     }
 214 }
 215
 216 real calc_xcm(rvec x[], int gnx, int *index, t_atom *atom, rvec xcm,
 217               gmx_bool bQ)
 218 {
 219     int  i, ii, m;
 220     real m0, tm;
 221
 222     clear_rvec(xcm);
 223     tm = 0;
 224     for (i = 0; (i < gnx); i++)
 225     {
 226         ii = index ? index[i] : i;
 227         if (atom)
 228         {
 229             if (bQ)
 230             {
 231                 m0 = std::abs(atom[ii].q);
 232             }
 233             else
 234             {
 235                 m0 = atom[ii].m;
 236             }
 237         }
 238         else
 239         {
 240             m0 = 1;
 241         }
 242         tm += m0;
 243         for (m = 0; (m < DIM); m++)
 244         {
 245             xcm[m] += m0*x[ii][m];
 246         }
 247     }
 248     for (m = 0; (m < DIM); m++)
 249     {
 250         xcm[m] /= tm;
 251     }
 252
 253     return tm;
 254 }
 255
 256 real sub_xcm(rvec x[], int gnx, int *index, t_atom atom[], rvec xcm,
 257              gmx_bool bQ)
 258 {
 259     int  i, ii;
 260     real tm;
 261
 262     tm = calc_xcm(x, gnx, index, atom, xcm, bQ);
 263     for (i = 0; (i < gnx); i++)
 264     {
 265         ii = index ? index[i] : i;
 266         rvec_dec(x[ii], xcm);
 267     }
 268     return tm;
 269 }
 270
 271 void add_xcm(rvec x[], int gnx, int *index, rvec xcm)
 272 {
 273     int  i, ii;
 274
 275     for (i = 0; (i < gnx); i++)
 276     {
 277         ii = index ? index[i] : i;
 278         rvec_inc(x[ii], xcm);
 279     }
 280 }
 281
 282 void orient_princ(t_atoms *atoms, int isize, int *index,
 283                   int natoms, rvec x[], rvec *v, rvec d)
 284 {
 285     int     i, m;
 286     rvec    xcm, prcomp;
 287     matrix  trans;
 288
 289     calc_xcm(x, isize, index, atoms->atom, xcm, FALSE);
 290     for (i = 0; i < natoms; i++)
 291     {
 292         rvec_dec(x[i], xcm);
 293     }
 294     principal_comp(isize, index, atoms->atom, x, trans, prcomp);
 295     if (d)
 296     {
 297         copy_rvec(prcomp, d);
 298     }
 299
 300     /* Check whether this trans matrix mirrors the molecule */
 301     if (det(trans) < 0)
 302     {
 303         for (m = 0; (m < DIM); m++)
 304         {
 305             trans[ZZ][m] = -trans[ZZ][m];
 306         }
 307     }
 308     rotate_atoms(natoms, NULL, x, trans);
 309     if (v)
 310     {
 311         rotate_atoms(natoms, NULL, v, trans);
 312     }
 313
 314     for (i = 0; i < natoms; i++)
 315     {
 316         rvec_inc(x[i], xcm);
 317     }
 318 }